You have to configure your HikaShop search plugin for products to look in those fields. Go to the plugin manager and look for the "Search - HikaShop Products" plugin. Then change which fields it uses when searching under fields, including your custom fields. See image attached.
Not sure if this will fix your Filters or if you need to do something else there. Depends on how you have them configured, as when you set up a filter you choose which fields it will use for each particular filter, including any custom fields.